Pope Francis has begged for forgiveness during a visit to Chile over the “irreparable damage” done to children who were raped and molested by priests in the country.

The Pope directly addressed a scandal that has greatly hurt the Catholic Church’s credibility in Chile and cast a cloud over his visit.

Francis also faced controversy on another front as three more Catholic churches were torched – two in the southern Araucania region where Francis will arrive on Wednesday to meet representatives of Chile’s indigenous people.

While not causing any injuries, nine church firebombings in the past few days have marked an unprecedented level of protest against history’s first Latin American pope on his home turf.

A woman is arrested during a protest against Pope Francis in Santiago (AP)

However, in Santiago, tens of thousands of jubilant Chileans turned out in droves for Francis’s first public Mass, a massive gathering in the capital’s O’Higgins Park where St John Paul celebrated Mass three decades ago.

Before the service began, Francis took a ride in his popemobile through the grounds to greet well-wishers, some of whom had camped out overnight to secure a spot.

In his first event of the day, Francis met privately with Chilean president Michelle Bachelet and addressed legislators, judges and other authorities at La Moneda palace.

They interrupted him with applause when he said he felt “bound to express my pain and shame” that some of Chile’s pastors had sexually abused children in their care.

Francis arrives to celebrate Mass at O’Higgins Park (AP)

“I am one with my brother bishops, for it is right to ask forgiveness and make every effort to support the victims, even as we commit ourselves to ensuring that such things do not happen again,” he said.

Francis did not refer by name to Chile’s most notorious paedophile priest, the Rev Fernando Karadima, who was sanctioned in 2011 by the Vatican to a lifetime of “penance and prayer” for sexually molesting minors.

Nor did he refer to the fact that the emeritus archbishop of Santiago, a top papal adviser, has acknowledged he knew of complaints against Karadima but did not remove him from ministry.

Karadima had been a politically connected, charismatic and powerful priest who ministered to a wealthy Santiago community and produced dozens of priestly vocations and five bishops.

The Pope waves as he arrives at the San Luis Beltran church on his way to the Apostolic Nunciature in Santiago (AP)

Victims went public with their accusations in 2010, after complaining for years to church authorities that Karadima would kiss and fondle them when they were teenagers.

While the scandal rocked the church, many Chileans are still furious over Francis’ subsequent decision, in 2015, to appoint a Karadima protege as bishop of the southern city of Osorno. Bishop Juan Barros has denied knowing about Karadima’s abuse but many Chileans do not believe him, and his appointment has badly split the diocese.

The pope will try to inject new energy into the church during his visit, which includes sessions with migrants, members of Chile’s Mapuche indigenous group and victims of the 1973-1990 military dictatorship. It remains to be seen if he will meet with sex abuse survivors.